My 2nd daughter used to run away from school, the teachers would literally have to chase her down a busy street! there were times she went to school in her underwear and a t-shirt, hair not brushed the whole nine yards, hers was a little different situation, her dad and I just got back togather and he had two other children, I got robbed at gun point where I worked, and although she was 6 at the time she knew what all this meant. It took a lot of work on mine and the schools part (we lived in Los Angeles at the time).But we did manage.
Know to your son, like parents ahead said first make sure that nothing is going on at school that would be upsetting him, once you know that he is ok and no one is bullying him, set a plan of action, If there is no fever he doesn't stay home or leave school period, make sure you get the school on board, He may sit in the office for 20 min but then he must go back to class, no exceptions, he has learned a tool that lets him get his way and know it needs to be broken, if he does manage to get his way and come home then it is into bed no t.v which you do, and very limited interaction, you want to make being home as miserable as you can, he may leave bed for the bathroom and to eat but thats it, it will be hard at first, but stick with it, I do this with any of mine who pull this stunt on me, and after a few times most don't try it again, I also reward with one day off of school, per semester so long as thier grades are up and they have no other unnecassary absences, on that day we do something fun, w/ 7 kids I had to get creative in how I got to spend a little one on one time w/ them, and that really seems to work, Your moms instinct will tell you when something is really wrong, but I always start with a fever, if there isn't one then the odds are good they are OK, my 15 year old boy is a bit of a hypocondracte also and what I always say when he has a complaint is sorry to hear it let me know if it gets worse tomorrow, I usually don't hear that complaint but of course there is always a new one LOL he broke his collar bine during a football game and when he first called I was like Ok I'll see you when you get home (it was an away game) he gets home and it was slightly swollen so I new it was injured but I made hime wait until the next morning (only 5 hours), I took him in cause the swelling hadn't gone down, and it was broken but because he exagerates everthing at times it can be hard, don't ever feel guilty for questioning the seriousness of what they say, it can be at times a guessing game, but I do listen to my insticnt, and it hasn't failed me yet. I know this is long and sorry for that, oh by the way my daughter is and almost A student in the 10th grade know so there is hope for your son, he just needs to be redirected and know that school isn't optional, it is mandatory under any circumstance.